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NMR Facility

We have worked with King's NMR Facility to provide users of the facility with a complmentary suite of analysis software made available through CREATE. This page provides a list of this software and guidance on how to access it. Depending on the nature of the software we recommend running it on the NMR Facility virtual desktop server (for GUI based analysis tools) or CREATE HPC (for long running simulations launched via scheduler).

GUI applications

The NMR Facility has a dedicated server with 64 CPU cores and 250GB of memory. It has been deployed within CREATE Cloud as a virtual desktop server for running interactive GUI based analysis tools.

  • Access to the server can be requested from the NMR Facility Manager (james.jarvis@kcl.ac.uk)
  • Once access is granted you can click "view in browser" here to launch a virtual desktop, logging in with your k-number and King's password
  • The shared storage on this server is the same as CREATE HPC
    • Your home directory is backed up and has a 50 GiB quota
    • You also have access to 200GiB of non-backed up "scratch" at /scratch/users/<your k number>
    • Registered research projects are entitled
  • Applications (command to launch from terminal/menu, application website)
    • /opt/ccpnmr2.5.2/bin/analysis, https://sites.google.com/site/ccpnwiki/home/documentation/ccpnmr-analysis
    • /opt/ccpnmr3.2.0/bin/assign, https://ccpn.ac.uk/support/tutorials/
    • /opt/nmrpipe/nmrbin.linux235_64/nmrPipe, https://www.ibbr.umd.edu/nmrpipe/
    • Applications -> Education -> PyMOL Molecular Graphics System, https://pymol.org
  • This server also has access to HPC applications via the module system, for example module load matlab; matlab

HPC applications

For running longer simulations without a GUI the CREATE HPC cluster has a larger number of high CPU count, high memory and GPU compute nodes available to all KCL researchers. Get access, connect over SSH and begin running jobs. e-Research also offers introductory HPC training (a registration link for upcoming training notices will be documented here soon).

Applications are available via modules. Modules of note for NMR Facility users:

  • xplor-nih, https://nmr.cit.nih.gov/xplor-nih/
  • matlab

Other software:

  • YASARA, http://www.yasara.org/, this software is best installed indvidually in your home directory or personal scratch space, simply acquire the latest version from the website and run install_yasara in one of those locations

Application backlog

We are still working on making the following software available.

  • CS-Rosetta
  • UNIO
  • ARIA
  • CNS 1.21
  • HyCUD